A [i]genome[/i] contains the sequence data for a particular individual organism. Genus of the relevant organism. RandParam('streptococcus', 'staphyloccocus', 'felis', 'homo', 'ficticio', 'strangera', 'escherischia', 'carborunda') Species of the relevant organism. StringGen('PKVKVKVKVKV') The unique characterization identifies the particular organism instance from which the genome is taken. It is possible to have in the database more than one genome for a particular species, and every individual organism has variations in its DNA. StringGen('PKVKVK999') The access code determines which users can look at the data relating to this genome. Each user is associated with a set of access codes. In order to view a genome, one of the user's access codes must match this value. RandParam('low','medium','high') TRUE if the genome is complete, else FALSE The taxonomy string contains the full taxonomy of the organism, while individual elements separated by semi-colons (and optional white space), starting with the domain and ending with the disambiguated genus and species (which is the organism's scientific name plus an identifying string). join('; ', (RandParam('bacteria', 'archaea', 'eukaryote', 'virus', 'environmental'), ListGen('PKVKVKVK', 5), $this->{genus}, $this->{species})) The group identifies a special grouping of organisms that would be displayed on a particular page or of particular interest to a research group or web site. A single genome can belong to multiple such groups or none at all. This index allows the applications to find all genomes associated with a specific access code, so that a complete list of the genomes users can view may be generated. This index allows the applications to find all genomes for a particular species. A [i]source[/i] describes a place from which genome data was taken. This can be an organization or a paper citation. URL the paper cited or of the organization's web site. This field optional. "http://www.conservativecat.com/Ferdy/TestTarget.php?Source=" . $this->{id} Description the source. The description can be a street address or a citation. $this->{id} . ': ' . StringGen(IntGen(50,200)) A [i]contig[/i] is a contiguous run of residues. The contig's ID consists of the genome ID followed by a name that identifies which contig this is for the parent genome. As is the case with all keys in this database, the individual components are separated by a period. [p]A contig can contain over a million residues. For performance reasons, therefore, the contig is split into multiple pieces called [i]sequences[/i]. The sequences contain the characters that represent the residues as well as data on the quality of the residue identification. A [i]sequence[/i] is a continuous piece of a [i]contig[/i]. Contigs are split into sequences so that we don't have to have the entire contig in memory when we are manipulating it. The key of the sequence is the contig ID followed by the index of the begin point. String consisting of the residues. Each residue is described by a single character in the string. RandChars("ACGT", IntGen(100,400)) String describing the quality data for each base pair. Individual values will be separated by periods. The value represents negative exponent of the probability of error. Thus, for example, a quality of 30 indicates the probability of error is 10^-30. A higher quality number a better chance of a correct match. It is possible that the quality data is not known for a sequence. If that is the case, the quality vector will contain the [b]unknown[/b]. unknown A [i]feature[/i] is a part of a genome that is of special interest. Features may be spread across multiple contigs of a genome, but never across more than one genome. Features can be assigned to roles via spreadsheet cells, and are the targets of annotation. Code indicating the type of this feature. RandParam('peg','rna') Alternative name for this feature. A feature can have many aliases. StringGen('Pgi|99999', 'Puni|XXXXXX', 'PAAAAAA999') [i](optional)[/i] A translation of this feature's residues into character codes, formed by concatenating the pieces of the feature together. For a protein encoding group, this is the protein characters. For other types it is the DNA characters. Upstream sequence the feature. This includes residues preceding the feature as well as some of the feature's initial residues. TRUE if this feature is still considered valid, FALSE if it has been logically deleted. 1 Web hyperlink for this feature. A feature have no hyperlinks or it can have many. The links are to other websites that have useful about the gene that the feature represents, and are coded as raw HTML, using [b]<a href="[i]link[/i]">[i]text[/i]</a>[/b] notation. 'http://www.conservativecat.com/Ferdy/TestTarget.php?Source=' . $this->{id} . "&Number=" . IntGen(1,99) This index allows the user to find the feature corresponding to the specified alias name. A [i]role[/i] describes a biological function that may be fulfilled by a feature. One of the main goals of the database is to record the roles of the various features. EC code for this role. StringGen(IntGen(20,40)) . "(" . $this->{id} . ")" Abbreviated name for the role, generally non-unique, but useful in column headings for HTML tables. This index allows the user to find the role corresponding to an EC number. An [i]annotation[/i] contains supplementary information about a feature. Annotations are currently the only objects that may be inserted directly into the database. All other information is loaded from data exported by the SEED. [p]Each annotation is associated with a target [b]Feature[/b]. The key of the annotation is the target feature ID followed by a timestamp. Date and time of the annotation. Text of the annotation. A [i]reaction[/i] is a chemical process catalyzed by a protein. The reaction ID is generally a small number preceded by a letter. HTML string containing a link to a web location that describes the reaction. This field is optional. TRUE if this reaction is reversible, else FALSE A [i]compound[/i] is a chemical that participates in a reaction. All compounds have a unique ID and may also have one or more names. Priority of a compound name. The name with the loweset priority is the main name of this compound. Descriptive name for the compound. A compound may have several names. Chemical Abstract Service ID for this compound (optional). Name used in reaction display strings. It is the same as the name possessing a priority of 1, but it is placed here to speed up the query used to create the display strings. This index allows the user to find the compound corresponding to the specified name. This index allows the user to find the compound corresponding to the specified CAS ID. This index allows the user to access the compound names in priority order. A [i]subsystem[/i] is a collection of roles that work together in a cell. Identification of subsystems is an important tool for recognizing parallel genetic features in different organisms. Name of the person currently in charge of the subsystem. Descriptive notes about the subsystem. A [i]role subset[/i] is a named collection of roles in a particular subsystem. The subset names are generally very short, non-unique strings. The ID of the parent subsystem is prefixed to the subset ID in order to make it unique. A [i]genome subset[/i] is a named collection of genomes that participate in a particular subsystem. The subset names are generally very short, non-unique strings. The ID of the parent subsystem is prefixed to the subset ID in order to make it unique. Part of the process of locating and assigning features is creating a spreadsheet of genomes and roles to which features are assigned. A [i]spreadsheet cell[/i] represents one of the positions on the spreadsheet. A [i]user[/i] is a person who can make annotations and view data in the database. The user object is keyed on the user's login name. Full name or description of this user. Access code possessed by this user. A user can have many access codes; a genome is accessible to the user if its access code matches any one of the user's access codes. RandParam('low', 'medium', 'high') A [i]property[/i] is a type of assertion that could be made about the properties of a particular feature. Each property instance is a key/value pair and can be associated with many different features. Conversely, a feature can be associated with many key/value pairs, even some that notionally contradict each other. For example, there can be evidence that a feature is essential to the organism's survival and evidence that it is superfluous. Name of this property. Value associated with this property. For each property name, there must by a property record for all of its possible values. This index enables the application to find all values for a specified property name, or any given name/value pair. A functional diagram describes the chemical reactions, often comprising a single subsystem. A diagram is identified by a short name and contains a longer descriptive name. The actual diagram shows which functional roles guide the reactions along with the inputs and outputs; the database, however, only indicate which roles belong to a particular map. Descriptive name of this diagram. An external alias is a feature name for a functional assignment that is not a FIG ID. Functional assignments for external aliases are kept in a separate section of the database. This table contains a description of the relevant organism for an external alias functional assignment. Descriptive name of the target organism for this external alias. An external alias is a feature name for a functional assignment that is not a FIG ID. Functional assignments for external aliases are kept in a separate section of the database. This table contains the functional role for the external alias functional assignment. Functional role for this external alias. A coupling is a relationship between two features. The features are physically close on the contig, and there is evidence that they generally belong together. The key of this entity is formed by combining the coupled feature IDs with a space. A number based on the set of PCHs (pairs of close homologs). A PCH indicates that two genes near each other on one genome are very similar to genes near each other on another genome. The score only counts PCHs for which the genomes are very different. (In other words, we have a pairing that persists between different organisms.) A higher score implies a stronger meaning to the clustering. A PCH (physically close homolog) connects a clustering (which is a pair of physically close features on a contig) to a second pair of physically close features that are similar to the first. Essentially, the PCH is a relationship between two clusterings in which the first clustering's features are similar to the second clustering's features. The simplest model for this would be to simply relate clusterings to each other; however, not all physically close pairs qualify as clusterings, so we relate a clustering to a pair of features. The key is the clustering key followed by the IDs of the features in the second pair. TRUE if this PCH is used in scoring the attached clustering, else FALSE. If a clustering has a PCH for a particular genome and many similar genomes are present, then a PCH will probably exist for the similar genomes as well. When this happens, only one of the PCHs will be scored: the others are considered duplicates of the same evidence. This relationship connects a feature to all the functional couplings in which it participates. A functional coupling is a recognition of the fact that the features are close to each other on a chromosome, and similar features in other genomes also tend to be close. Ordinal position of the feature in the coupling. Currently, this is either "1" or "2". This index enables the application to view the features of a coupling in the proper order. The order influences the way the PCHs are examined. This relationship connects a genome to all of its features. This relationship is redundant in a sense, because the genome ID is part of the feature ID; however, it makes the creation of certain queries more convenient because you can drag in filtering information for a feature's genome. Feature type (eg. peg, rna) This index enables the application to view the features of a Genome sorted by type. This relationship connects a functional coupling to the physically close homologs (PCHs) which affirm that the coupling is meaningful. This relationship connects a PCH to the features that represent its evidence. Each PCH is connected to a parent coupling that relates two features on a specific genome. The PCH's evidence that the parent coupling is functional is the existence of two physically close features on a different genome that correspond to the features in the coupling. Those features are found on the far side of this relationship. Ordinal position of the feature in the coupling that corresponds to our target feature. There is a one-to-one correspondence between the features connected to the PCH by this relationship and the features connected to the PCH's parent coupling. The ordinal position is used to decode that relationship. Currently, this field is either "1" or "2". This index enables the application to view the features of a PCH in the proper order. This relationship connects a genome to the contigs that contain the actual genetic information. This relationship connects a genome to the sources that mapped it. A genome can come from a single source or from a cooperation among multiple sources. A contig is stored in the database as an ordered set of sequences. By splitting the contig into sequences, we get a performance boost from only needing to keep small portions of a contig in memory at any one time. This relationship connects the contig to its constituent sequences. Length of the sequence. Index (1-based) of the point in the contig where this sequence starts. This index enables the application to find all of the sequences in a contig in order, and makes it easier to find a particular residue section. This relationship connects a feature to its annotations. This relationship connects an annotation to the user who made it. This relationship connects subsystems to the genomes that use it. If the subsystem has been curated for the genome, then the subsystem's roles will also be connected to the genome features through the [b]SSCell[/b] object. Code indicating the subsystem variant to which this genome belongs. Each subsystem can have multiple variants. A variant code of [b]-1[/b] indicates that the genome does not have a functional variant of the subsystem. A variant code of [b]0[/b] indicates that the genome's participation is considered iffy. This index enables the application to find all of the genomes using a subsystem in order by variant code, which is how we wish to display them in the spreadsheets. This relationship connects roles to the subsystems that implement them. Column number for this role in the specified subsystem's spreadsheet. This index enables the application to see the subsystem roles in column order. The ordering of the roles is usually significant, so it is important to preserve it. This relationship connects a subsystem's spreadsheet cell to the genome for the spreadsheet column. This relationship connects a subsystem's spreadsheet cell to the role for the spreadsheet row. This relationship connects a subsystem's spreadsheet cell to the features assigned to it. ID of this feature's cluster. Clusters represent families of related proteins participating in a subsystem. This relationship connects a reaction to the compounds that participate in it. TRUE if the compound is a product of the reaction, FALSE if it is a substrate. When a reaction is written on paper in chemical notation, the substrates are left of the arrow and the products are to the right. Sorting on this field will cause the substrates to appear first, followed by the products. If the reaction is reversible, then the notion of substrates and products is not at intuitive; however, a value here of FALSE still puts the compound left of the arrow and a value of TRUE still puts it to the right. Number of molecules of the compound that participate in a single instance of the reaction. For example, if a reaction produces two water molecules, the stoichiometry of water for the reaction would be two. When a reaction is written on paper in chemical notation, the stoichiometry is the number next to the chemical formula of the compound. TRUE if this compound is one of the main participants in the reaction, else FALSE. It is permissible for none of the compounds in the reaction to be considered main, in which case this value would be FALSE for all of the relevant compounds. An optional character string that indicates the relative position of this compound in the reaction's chemical formula. The location affects the way the compounds present as we cross the relationship from the reaction side. The product/substrate flag comes first, then the value of this field, then the main flag. The default value is an empty string; however, the empty string sorts first, so if this field is used, it should probably be used for every compound in the reaction. A unique ID for this record. The discriminator does not provide any useful data, but it prevents identical records from being collapsed by the SELECT DISTINCT command used by ERDB to retrieve data. This index presents the compounds in the reaction in the order they should be displayed when writing it in chemical notation. All the substrates appear before all the products, and within that ordering, the main compounds appear first. This relationship connects a feature to the contig segments that work together to effect it. The segments are numbered sequentially starting from 1. The database is required to place an upper limit on the length of each segment. If a segment is longer than the maximum, it can be broken into smaller bits. [p]The upper limit enables applications to locate all features that contain a specific residue. For example, if the upper limit is 100 and we are looking for a feature that contains residue 234 of contig [b]ABC[/b], we can look for features with a begin point between 135 and 333. The results can then be filtered by direction and length of the segment. Sequence number of this segment. Index (1-based) of the first residue in the contig that belongs to the segment. Number of residues in the segment. A length of 0 identifies a specific point between residues. This is the point before the residue if the direction is forward and the point after the residue if the direction is backward. Direction of the segment: [b]+[/b] if it is forward and [b]-[/b] if it is backward. This index allows the application to find all the segments of a feature in the proper order. This index is the one used by applications to find all the feature segments that contain a specific residue. This relationship is one of two that relate features to each other. It connects features that are very similar but on separate genomes. A bidirectional best hit relationship exists between two features [b]A[/b] and [b]B[/b] if [b]A[/b] is the best match for [b]B[/b] on [b]A[/b]'s genome and [b]B[/b] is the best match for [b]A[/b] on [b]B[/b]'s genome. ID of the genome containing the target (to) feature. score for this relationship This index allows the application to find a feature's best hit for a specific target genome. This relationship connects a feature to its known property values. The relationship contains text data that indicates the paper or organization that discovered evidence that the feature possesses the property. So, for example, if two papers presented evidence that a feature is essential, there would be an instance of this relationship for both. URL or citation of the paper or institution that reported evidence of the relevant feature possessing the specified property value. This relationship connects a role to the diagrams on which it appears. A role frequently identifies an enzyme, and can appear in many diagrams. A diagram generally contains many different roles. This relationship connects a subsystem to the spreadsheet cells used to analyze and display it. The cells themselves can be thought of as a grid with Roles on one axis and Genomes on the other. The various features of the subsystem are then assigned to the cells. This relationship identifies the users trusted by each particular user. When viewing functional assignments, the assignment displayed is the most recent one by a user trusted by the current user. The current user implicitly trusts himself. If no trusted users are specified in the database, the user also implicitly trusts the user [b]FIG[/b]. This relationship connects a role subset to the roles that it covers. A subset is, essentially, a named group of roles belonging to a specific subsystem, and this relationship effects that. Note that will a role may belong to many subsystems, a subset belongs to only one subsystem, and all roles in the subset must have that subsystem in common. This relationship connects a subset to the genomes that it covers. A subset is, essentially, a named group of genomes participating in a specific subsystem, and this relationship effects that. Note that while a genome may belong to many subsystems, a subset belongs to only one subsystem, and all genomes in the subset must have that subsystem in common. This relationship connects a subsystem to its constituent role subsets. Note that some roles in a subsystem may not belong to a subset, so the relationship between roles and subsystems cannot be derived from the relationships going through the subset. This relationship connects a subsystem to its constituent genome subsets. Note that some genomes in a subsystem may not belong to a subset, so the relationship between genomes and subsystems cannot be derived from the relationships going through the subset. This relationship connects a role to the reactions it catalyzes. The purpose of a role is to create proteins that trigger certain chemical reactions. A single reaction can be triggered by many roles, and a role can trigger many reactions.